The Mysterious Stranger is (As the perk says) Cywren's personal guardian angel. when using the V.A.T.S. the Mysterious Stranger will literally appear out of nowhere to assist Cywren by finishing off her enemies. After the V.A.T.S. sequence finishes, he will disappear in a similarly abrupt manner.
The Mysterious Stranger in Fallout 3 and Fallout: New Vegas is heavily implied to be the father of The Lonesome Drifter. In speech, the Drifter will state that his father was a "mysterious" man, and that he was a "stranger" to his own family. The word mysterious appears right above stranger in the dialogue box. The Drifter carries a unique .44 magnum, which can be acquired by the Courier, that looks remarkably like the Mysterious Stranger's revolver; and when drawing the revolver, the same guitar notes that are heard when the Mysterious Stranger shows up are played, and another note is played when the weapon is holstered.
His son makes a cameo in New Vegas.